ArticleMethods in molecular biology (Clifton, N.J.)2018
Targeted Sequencing of Respiratory Viruses in Clinical Specimens for Pathogen Identification and Genome-Wide Analysis.
Article in Methods in molecular biology (Clifton, N.J.), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Utilizing RT-PCR for infectious disease diagnosis with emphasis on non-tuberculous mycobacteria in Bangladesh, 2019-2024.BMC infectious diseases · 2026Article
- Clinicopathologic Features of Genitourinary Malakoplakia and Analytical Utility of the MetaPath Assay.Infection and drug resistance · 2026Article
- The application value of targeted next-generation sequencing in the diagnosis of primary osteoarticular infections: A single-center study.Frontiers in cellular and infection microbiology · 2025Article
- Evaluation of targeted next-generation sequencing for microbiological diagnosis of acute lower respiratory infection.Frontiers in microbiology · 2025Article
- Article
- A robust, scalable, and cost-efficient approach to whole genome sequencing of RSV directly from clinical samples.Journal of clinical microbiology · 2024Article
- Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases.Cells · 2023Review
- Field-based detection of bacteria using nanopore sequencing: Method evaluation for biothreat detection in complex samples.PloS one · 2023Article
- RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19.International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases · 2022Article
- Evaluation of targeted next-generation sequencing for detection of equine pathogens in clinical samples.Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc · 2021Article
- Comparison of Nucleic Acid Extraction Methods for a Viral Metagenomics Analysis of Respiratory Viruses.Microorganisms · 2020Article
- Enrichment post-library preparation enhances the sensitivity of high-throughput sequencing-based detection and characterization of viruses from complex samples.BMC genomics · 2019Article
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A large number of viruses can individually and concurrently cause various respiratory illnesses. Metagenomic sequencing using next-generation sequencing (NGS) technology is capable of identifying a variety of pathogens. Here, we describe a method using a large panel of oligo probes to enrich sequence targets of 34 respiratory DNA and RNA viruses that reduces non-viral reads in NGS data and achieves high performance of sequencing-based pathogen identification. The approach can be applied to total nucleic acids purified from respiratory swabs stored in viral transport medium. Illumina TruSeq RNA Access Library procedure is used in targeted sequencing of respiratory viruses. The samples are subjected to RNA fragmentation, random reverse transcription, random PCR amplification, and ligation with barcoded library adaptors. The libraries are pooled and subjected to two rounds of enrichments by using a large panel of oligos designed to capture whole genomes of 34 respiratory viruses. The enriched libraries are amplified and sequenced using Illumina MiSeq sequencing system and reagents. This method can achieve viral detection sensitivity comparable with molecular assay and obtain partial to complete genome sequences for each virus to allow accurate genotyping and variant analysis.
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